# Read me
## Progesterone on the day of AI and embryo quality

The dataset includes the 26 variables used in the published manuscript.
* id: cow id	
* trt: treatment applied during the original study	
* uid: id-trt-study (concat)	
* study: original study	code
* lact: parity
* bcsfinal: BCS d6 after AI
* cyclic: cyclicity at 30-44 DIM (assessed by ultrasound)
* folai: follicle size at AI
* heatai: heat signs at AI
* dbovai: double ovulation at AI
* duplicate: 2nd follicle/embryo
* grade: 1 = excellent and good, 2 = fair, 3 = poor, 4 = degenerated, 5 = NF
* asc: number of accessory sperm cells (zona pelicida)
* p4govs: [P4] at first GnRH
* p1ai: pregnancy on the next AI
* mast: mastitis during the study period
* e2ai: [E2] at AI	
* p4pgovs: [P4] at PG
* p4ai: [P4] at AI
* parity: parity coded as primiparous/multiparous
* p4flush: [P4] d6 after AI
* p4ai_cat: [P4] at AI categorized (threshold = 0.5 ng/mL)
* p4flush_cat: [P4] 6d after AI categorized (threshold = 2.0 ng/mL)
* p4pgovs_cat: [P4] at PG categorized (threshold = 2.0 ng/mL)
* asc_cat: number of accessory sperm cells categorized (threshold = 7)
* bcsfinal_cat: BCS d6 after AI (threshold = 2.5)
* e2ai_cat: [E2] at AI categorized (threshold = 3.0)

The R code includes details for descriptive statistics, cumulative
link mixed models, diagnostics, and plots.
